Wednesday, August 31, 2011

One of the ways to know whether your mathematical models of cosmology are correct is to run simulations and see whether they align with the observable universe. A team of researchers from the University of Zurich (Lucio Mayer) and from the University of California at Santa Cruz (Javiera Guedes, Simone Callegari and Piero Madau) has done just that. The results will be published in the Astrophysical Journal.

You can watch the simulation below.

When creating a mathematical model, it’s not only important that the simulation be internally consistent, but also that it match reality. You can judge for yourself whether the astronomers have achieved that goal.

Left: an image of our simulated galaxy, with gas in red and stars in blue.

Right: a picture in false colors of the galaxy M74, again with gas shown in red and stars in blue. The spiral arms of the gas are evident in both images.

Tuesday, August 30, 2011

Here’s a research project everyone can get behind. Scientists from the University of Leeds have synthesized a peptide (P11-4) that can repair the tiny lesions caused by tooth decay. When spread over teeth, the peptide coating not only protects the enamel from further decay, but even seems to recruit calcium and other minerals to the site to rebuild the teeth.

The tests were done on teeth that had been previously extracted by orthodontists. The scientists created caries-like lesions by exposing the teeth to acid solutions. They then painted the tooth surfaces with P11-4 peptides. After P11-4 was allowed to soak into the teeth, the teeth were subjected to further rounds of acid treatment to see whether the lesions would grow.

The in vitro results were extremely promising. Not only did the demineralization stop, but P11-4 also served as a scaffold for remineralization. Needless to say, the in vivo results may differ. The microenvironment of a tooth inside a human mouth is not going replicate that of a controlled mineral bath. However, if the results do pan out, dentists may one day paint peptide solutions on our teeth instead of drilling.

The team presented 500 breath samples (one fifth of which were from lung cancer patients) to a group of trained sniffer dogs. The dogs correctly identified 71 of the lung cancer patients (yielding a false negative score of 29%) and 372 of the healthy volunteers (false positive of only 7%). Unfortunately, the dogs have been unsuccessful at communicating which specific chemicals they were using to discriminate between healthy and sick people, making it extremely difficult to refine their training, or to design electronic sensors for lung cancer.

If these numbers can be improved, and great care is taken not to confound the results by influencing the dogs in any way (see my prior post about sniffer dogs), this might be a viable screening tool. Personally, I look forward to receiving a notice from my doctor that I ‘pass the sniff test’.

The prevailing theory is that the moon was created from the aftermath of a collision between a Mars-sized object and the early Earth. That part of the theory is not in question. It's what happened next that may need to be revisited.Currently, most astronomers believe that the collision caused the ejection from the Earth’s surface of an ocean of magma. This molten material found itself in orbit around the Earth where it slowly solidified from the inside out.

As the moon cooled, the lighter rocks floated to the surface and became the oldest rocks in the moon’s crust. One such rock, ferroan anorthosite (FAN) was brought back by the Apollo astronauts. Previous attempts to date the FAN samples have been inconsistent, but new techniques used by Lars Borg of Lawrence Livermore National Laboratory and his colleagues from the University of Copenhagen, Carnegie Institution and Clermont Université have yielded uniform results. The oldest lunar rocks are about 210 million years younger than previously thought.

Although a difference of less than 5% may not seem like a big deal, it means that the moon’s surface did not form at the time we thought it did. Either the moon solidified later, in which case the entire moon is younger than we thought, or the moon’s crust was not the product of a cooling magma ocean.

Saturday, August 27, 2011

Former fisheries graduate student Iori Tomita used red and blue dyes to study the bone structure of his captured specimens. In doing so, he created a new art form that has been on display at the Tokyo Institute of Technology. If you live in Japan and are interested in owning one of the pieces, they can be purchased from Tomita's website.

Although O2 is an abundant and critical part of Earth’s atmosphere today, this wasn’t always the case. About 2.3 billion years ago, the ‘Great Oxidation Event’ (GOE) forever changed the composition of our air, and led to the evolution of all complex life on Earth today*. However, there is some indication in the fossil record that organisms were using O2 as long as 2.6 billion years ago, before there was any noticeable amount available. Could such tiny amounts of O2 trigger a change from an anaerobic to an aerobic lifestyle? To answer that question, the MIT team grew modern yeast cells under varying conditions.

Without oxygen, yeast cells require ergosterol in their growth medium, but if O2 is present they will switch to metabolizing glucose. The team provided yeast cells with an anaerobic, or oxygen-free, environment in which to live. The growth medium contained both ergosterol and radioactively labeled glucose. They then provided tiny amounts of oxygen. They yeast began metabolizing the carbon13 labeled glucose when O2 levels were barely detectable.

This suggests that aerobic metabolisms may have evolved on Earth long before the GOE. Even negligible levels of O2 in isolated pockets of the Earth’s early oceans may have been utilized by opportunistic organisms.

Thursday, August 25, 2011

Many parasites have complicated lifecycles requiring specific hosts at specific stages. Toxoplasma gondii, the parasite responsible for toxoplasmosis, is no exception. It can only reproduce sexually while within the intestines of a cat. Unfortunately for the parasite, it periodically itself excreted from its preferred home, and thence into a less desirable host, such as a rat. It then falls to T. gondii to persuade the rat to get it back into a cat. Patrick House and Robert Sapolsky of Stanford are one step closer to understanding how this is accomplished.

The researchers found that while exposure to cat urine triggers fear and avoidance pathways in unaffected rat brains, male rats infected with T. gondii are attracted to cat urine in the same way that they are attracted to female rats. This was not true for other types of predatory urine. Apparently, T. gondii has no interest in getting rats into dogs or owls.

Exactly how this mind control is exerted is not yet known. However, T. gondii has been found in neurons, as shown below. T. gondii has also been known to raise dopamine levels by up to 15%. Taken together, it’s clear that the parasite is able to exert its influence directly on the brain.

By the way, toxoplasmosis is extremely common in humans. Although most people with the disease display few symptoms, there is a growing body of work suggesting that infected people display differences from the uninfected population in terms of their degree of aggression, neuroticism and love of cats.

Wednesday, August 24, 2011

In addition to gases, our lower atmosphere contains a large variety of bacteria. These bacteria get blown into the air from a number of sources, such as soil, dust, leaves and debris. What you probably don’t want to know is that a surprisingly large amount of aerosol bacteria come from dog feces.

Noah Feirer at the University of Boulder and his colleagues analyzed the bacterial content in 96 near-surface atmospheric samples from four Midwestern cities. They compared the DNA content in those samples to the DNA in databases of bacterial communities found in leaf litter and other potential sources, including human, cow and dog feces. They found a strong match to the dog poop bacteria, particularly in atmospheric samples taken during winter.

Other than taking greater care to quickly pick up after our pets, I’m not sure what can be done about this. Unfortunately, this is probably not the worst thing we’re going to find in our air.

Cavities, or dental caries, are actually bacterial infections of the teeth. By the time children reach preschool age, more than a quarter of them will already have cavities. For this reason, the researchers decided to see whether they could detect caries-causing bacteria in infants even before the children have any teeth. The answer was that they could.

Swanson’s team sequenced the DNA of all the salivary bacteria found in five toothless babies and their mothers. About 400 different bacterial genera were present in the samples. Although infants had only about half as many types of bacteria as the adults, they still had more than enough of the caries-causing pathogens to infect their teeth as they erupted.

Obviously, this was an extremely small study. More work must be done to see whether differences in feeding practices can affect the results. However, the results do suggest that in order to prevent cavities, oral care should begin even before children have any teeth.

First, a Lagrange or libration point is the position where an object such as moon can remain stationary relative to two larger bodies. Each two-body system has five such points. In the diagram below, if Mass1 is the sun and Mass2 is the Earth, L1 through L5 represent the Lagrange points of that system. A Trojan asteroid or moon orbits one of those Lagrange points. Although the asteroid may lie in the path of the orbiting planet, it can never collide with that planet because it is always in front of or behind the planet.

Trojan asteroids have been seen in the orbits of Jupiter and Saturn, but never before in Earth’s orbit. One would have to detect an exceedingly small object in the full glare of the sun to find one. Thanks to the WISE telescope, astronomers were able to do just that. At only 300 meters in diameter, asteroid 2010 TK7 is tiny indeed. It travels around one of Earth’s Lagrange points, maintaining a distance of about 80 million kilometers from Earth.

This artist's concept illustrates the first known Earth Trojan asteroid, discovered by NEOWISE, the asteroid-hunting portion of NASA's WISE mission. The asteroid is shown in gray and its extreme orbit is shown in green. Earth's orbit around the sun is indicated by blue dots. The objects are not drawn to scale.

Image credit: Paul Wiegert, University of Western Ontario, Canada.

If like me, you had difficulty visualizing the path a Trojan asteroid would take around the sun, the following animation may help.

Sunday, August 21, 2011

Here’s another story that could be filed under surprising results. People who are exposed to story spoilers may enjoy the subsequent plot more than those who were not tipped off ahead of time. This was true even for mysteries and thrillers.

Nicholas Christenfeld and Jonathan Leavitt of the University of California at San Diego took 12 classic short stories, many of which were either pure mysteries or contained at least one surprising twist, and added some spoilers to the beginning. Each version of each story (spoiled and unspoiled) was read by at least 30 volunteers (none of whom had prior familiarity with the works).

In all cases, the readers significantly preferred the spoiled versions, even when the introductory paragraph gave away the answer to the mystery or ‘ruined’ the surprise ending. Apparently, knowing who done it ahead of time can actually enhance the pleasure of reading a mystery, rather than detracting from it.

It’s not clear why this should be so. One possibility advanced by the researchers is that the main enjoyment derived from a story does not come from the plot itself, but rather from the way a storyteller crafts his words. If so, a spoiler may actually create anticipation to see how the author will take the reader to the pre-revealed end.

A few caveats for those eager to embrace this new license to spoil. First, not all spoiling is equal. For example, when the scientists tried inserting the spoiler paragraph into the center of the story rather than at the very beginning, readers didn’t like it as much. Second, this result may not hold true for movies or plays. And finally, it will probably make people mad when you spoil their books or movies for them, even if you explain that you’ve just done them a favor.

Saturday, August 20, 2011

Matthew Thompson, an undergraduate at the University of Queensland, came across this illusion, subsequently dubbed the 'Flashed Face Distortion Effect'. See if for yourself below.

Differences from the mean (slightly larger eyes, for example) become grotesquely exaggerated as the faces flash by. If you pause the clip, you can see that there are no monsters in lineup, just regular people.

Friday, August 19, 2011

For an object that is no longer classified as a planet, Pluto has been accumulating moons of its own. I thought Pluto only had one moon, Charon, which incidentally is almost half the size of Pluto. Apparently, I missed the news about moons two and three, Nix and Hydra. Now astronomers using the Hubble telescope have identified a fourth moon, name to be determined.

At around 20 kilometers across, the new moon, temporarily designated P4, is tiny. Nix and Hydra are each closer to 70 kilometers in diameter, which is still small enough to walk across in a few days. In comparison, Charon is about 1000 kilometers across and Pluto itself has a diameter of about 2300 kilometers.

These two images, taken about a week apart by NASA's Hubble Space Telescope, show four moons orbiting the distant, icy dwarf planet Pluto. The green circle in both snapshots marks the newly discovered moon, temporarily dubbed P4, found by Hubble in June.

Credit: NASA, ESA, and M. Showalter (SETI Institute).

BTW, Nix and Hydra were also discovered using the Hubble back in 2005.

Nutrient foramens are the tiny holes in bones that allow blood to enter and nourish the cells inside the bone. More active animals require a greater nutrient supply to their bone cells, and thus have larger nutrient foramens. In general, mammals have foramens that are ten times larger than those of comparably sized reptiles. This increase in size correlates well with maximum metabolic rates.

Next, the researchers determined the sizes of the nutrient foramens in fossilized dinosaur bones. They surveyed ten species, which included quadrupeds and bipeds, carnivores and herbivores. Surprisingly, the nutrient foramens in all ten species were larger than those of mammals!

There is mounting evidence that dinosaurs were not cold-blooded, but could control their internal temperatures. This new data suggests that, far from being sluggish lumberers, they may have led extremely active lives.

Some hospital patients must be isolated for either the patient’s or the caretaker’s safety. They might be severely immunocompromised, or extremely contagious. In either case, health care professionals must don gloves and gowns each time they enter such a patient’s room, even if they only need a brief consultation with the patient.

So how does duct tape figure into this? The researchers used red duct tape to create a three-foot square box on the floor at the threshold of each contact-restricted patient’s door. Health care professionals within this Red Box zone can safely speak to patients without needing to put on masks or gloves. Of course, more prolonged assessments or any procedures that required touching patients would still require a health care professional to suit up. But often that type of close contact is not necessary.

Aside from saving time and money, the new system has some additional benefits. Patients may feel more comfortable speaking to someone who is not wearing a mask. Also, the red duct tape on the floor serves as an additional cue to warn anyone entering the room to take contact precautions.

The blood-brain barrier is composed of endothelial cells which are packed much more tightly than in the rest of the body. Any molecule that makes its way into the brain must first pass through these tight junctions. This effectively protects the brain from pathogens or large molecules. Astrocytes make up an important cellular support system for the endothelial cells.

The scientists, led by Joan Berman, found that HIV-infected astrocytes can compromise the integrity of the blood-brain barrier. The infected astrocytes both passively allowed their endothelial clients to die, and emitted toxic signals killing neighboring astrocytes. Both events lead to gaps in the blood-brain barrier, which may in turn be the cause of the neurological problems.

Not surprisingly, this work has not been done in humans, but in macaque monkeys and in human cells. Nevertheless, the authors suggest that treatments that protect astrocytes may reduce HIV-related dementia.

Monday, August 15, 2011

Conventional wisdom holds that planetary systems form as clouds of dust and gas coalesce into a central star and orbiting planets. If true, then the star and all the planets, moons, asteroids, etc that originated from that cloud should be composed of the same atomic elements. According to a couple of new papers, this is not the case.

Both studies outlined differences in isotope ratios found in the solar wind (particles ejected from the sun’s atmosphere) from those found on Earth. Many elements come in different flavors, or isotopes, depending on how many neutrons they have. For example, oxygen always has eight protons, but may have eight (O16), nine (O17) or ten (O18) neutrons. In the same way, nitrogen has seven protons, but seven (N14) or eight (N15) neutrons. Some isotopes are common and others are exceedingly rare. However, the researchers expected to find that the ratios of isotopes coming from the sun would be the same as the ratios found on Earth. Not so.

The first paper, by Kevin McKeegan of UCLA and his colleagues, outlined differences in oxygen isotope ratios found in the solar wind compared to those found here on Earth. In the second paper, Bernard Marty of Nancy Université and his colleagues looked at nitrogen isotope ratios with the same result. In other words, the present isotopic makeup of the Earth does not match the solar material from which it was presumed to have co-formed.

In order to determine what effect giving specific directions would have on children’s creativity, the researchers built a colorful, gadgety toy with four hidden functions. Pulling or pressing parts of it could make it squeak, light up or play musical notes, and looking down one of the tubes would reveal a reverse mirrored image. 85 preschoolers were recruited to play with the new toy under four different conditions.

One group (pedagogical) was explicitly shown one function (how to make the toy squeak). The second group (interrupted) was also shown how to operate the squeak function, but the experimenter immediately excused herself (claiming to have forgotten something important) and left the area. For the third group (naive), the experimenter pretended to have just figured out the squeak function by accident. Finally, the fourth group of children was simply offered the toy with little comment. Each of the children was then left alone to examine and play with the toy.

Gabriella, 5, plays with the researchers' toy in the PlayLab at Boston's Children's Museum.

Photos: Patrick Gillooly.

The group that was least likely to discover even one other function of the toy was the pedagogical group. The authors speculate that when someone is explicitly taught how to use an object, he or she assumes that that’s all there is to it. These same children also spent much less time playing with toy.

This reminds me of a parental dilemma. I’ve often thought, upon stumbling across something I was sure my young child would find fascinating, that the best scenario would be for her to discover it on her own. Barring that, would it be better to point it out to her (and risk diminishing her interest) or hope that she would one day find it without help (and risk that she never would)?

When a person is infected, phagocytes, or polymorphonuclear leukocytes (PMNs) are activated. However, PMNs undergo changes depending on whether the infections they are fighting are viral or bacterial. These changes can be detected by chemiluminescence screening in much less time than it would take to culture the infection and observe it directly.

Thus far, the researchers have achieved an almost 90% success rate in classifying infections as of either viral or bacterial origin. They hope their work will lead to faster and more accurate treatments.

Thursday, August 11, 2011

Eyes have evolved independently in different lineages up to a hundred times during the course of life on Earth. Until recently, there has been little evidence of complex eyes dating back to the early Cambrian, which began 540 million years ago. Now, Australian paleontologists Michael Lee and John Paterson and their colleagues have found evidence of extremely complex compound eyes dating to about 515 million years ago.

A half-billion-year-old fossil compound eye, showing exquisite detail of the visual surface (the individual lenses can be seen as darker spots).

Credit: Photo by John Paterson (University of New England).

Most of the major phyla present today first appeared during the Cambrian ‘explosion’. Although many of these early organisms would have had eyes, few of the eyes have been preserved, with the exception of the biomineralized eyes of trilobites. In contrast, the recently discovered fossils were of compound eyes made up of over 3000 lenses (shown as 'pixels' below). In comparison, living horseshoe crabs have compound eyes made up of 1000 lenses, whereas dragonflies are the visual champions with 28,000 lenses.

The researchers are not sure to which creature the eyes belonged, but suspect that it was an active predator, given that many of its contemporaries, such as trilobites, had eyes with only 100 or so lenses. You can see what a difference this makes below:

Images as seen by (left to right) Cambrian trilobite, newly found fossilized eye, modern dragonfly.

Notice that, contrary to a commonly held myth, each lens does not provide a separate picture of the whole visual field but rather a tiny section of the visual field. The more lenses (or pixels) available, the higher the picture resolution. This makes sense if you think about it. Seeing one image in greater resolution could give an animal a clear advantage. It's hard to imagine what advantage would be gained by seeing 28,000 tiny separate images.

Wednesday, August 10, 2011

Watch the following clip. Does Rocky the yellow jacket (the University of Rochester mascot) appear to be expanding? It’s actually completely still. Our brains perceive that outward motion because it’s in the opposite direction of the inward moving lines.

According to research by Duje Tadin and his colleagues from the University of Rochester and from McGill University, as little as 25 milliseconds will trigger this illusion, known as the motion aftereffect. Even after the most fleeting exposure to movement, neurons in the motion center of the brain respond to stationary objects as if they too were in motion.

Because there is virtually always some background movement in our visual field, the authors expect this phenomenon to occur almost continuously. Their next goal is to figure out what if any advantage this might provide.

Tuesday, August 9, 2011

David Phillips and Kimberly Brewer (no pun intended) of the University of California, San Diego used data from the Fatality Analysis Reporting System (FARS) to compare blood alcohol contents (BAC, expressed as the percentage of alcohol in blood) in drivers involved in accidents. They concluded that even a BAC of 0.01 (one hundredth of one percent of the blood is alcohol) correlated with an increase in the severity of accidents.

The researchers used FARS data from 1994 to 2008, involving almost one and a half million people. FARS covers every fatal accident in the country, and records BAC down to 0.01. In the U.S., the legal BAC driving limit is 0.08 (many other countries have much lower limits). Phillips and Brewer found that the higher the BAC, the greater the chance that an accident would be a severe one. Even with a BAC of only 0.01, the ratio of severe injury to non-injury accident went up by a third, compared to accidents with sober drivers.

This is bad news for people who feel they can safely have one or two drinks with dinner before getting in a car. It turns out that the safest amount of alcohol for a driver is no alcohol.

Monday, August 8, 2011

I’ve written before about markers that allow forensic scientists to age the donators of blood stains to within nine years. Now UCLA researchers have found completely different age markers in saliva.

The blood study relied on the accumulation of a by-product of T-cell function. This time, the scientists looked at the DNA itself, or more specifically, the amount of methylation of that DNA within saliva samples. The researchers compared the DNA of 34 sets of identical male twins and found 88 sites that correlated methylation with age. In other words, the older the man was, the more likely those sites were to be methylated. This held true in a later study of 31 men and women aged 18 to 70. In fact, the researchers were able to estimate most people’s ages to within five years.

It’s just a matter of time before dating services start offering saliva-authenticated proof of age certificates.

Sunday, August 7, 2011

‘Boosting’ your immune system may be the last thing you want to do if you have a cold, at least if you’re asthmatic. According to a study led by Marc Hershenson from the University of Michigan Medical School, mice with a reduced immune response to cold viruses had less airway inflammation and bronchoconstriction during infection.

In the process of clearing our bodies of foreign invaders, our immune systems can sometimes cause more trouble than they’re worth. For example, it is the immune response, not the infection, which is responsible for inflammation. And it is certainly the immune response that causes allergic and autoimmune symptoms. Apparently, it is also the immune system that exacerbates cold-induced asthma.

As Hershenson explains:

In our model, cold-induced asthma flare-ups were caused by the body's immune response to the virus, not the virus itself. Chemicals produced by the immune system inflame cells and tissues, causing asthma symptoms such as cough and wheeze.

Sure enough, mice that were immuno-deficient had less airway problems following infection with a cold virus than did mice with a normal immune response. Of course, mice with no immune response could not fight off infections at all, so clearly a middle ground is best.

Saturday, August 6, 2011

Gary Greenberg, the director of the Microscopy & Microanalysis Laboratory at the University of Hawaii Institute for Astronomy in Maui, HI, is a sand artist. No, he doesn't make elaborate sculptures out of sand. Instead, he photographs sand grains using a high definition, 3D light microscope he invented as a professor at the University of Southern California. The results are surprisingly beautiful. In fact, he published a book about them, called A Grain of Sand.

Stochastic Scientist? What's up with that?

Why the Stochastic Scientist? As I'm sure you all know, 'stochastic' is another word for 'random', which is what I intend for the focus of this blog. Although my formal training is as a molecular biologist, there are many other fields of science that are also fascinating and beautiful. It's my intention to blog about which ever scientific discovery or invention catches my, and hopefully your, fancy.

I also hope to inspire people to learn more about science. By choosing among a huge variety of scientific endeavors, I'll undoubtably hit upon something that will pique my readers' interest.

I guess I could have called my blog 'The Joy of Science', but that wouldn't have been quite so random.